In this paper, we present a study of second graders’ learning about the nature of matter in the context of content‐rich, model‐based inquiry instruction. The goal of instruction was to help students learn to use simple particle models to explain states of matter and phase changes. We examined changes in students’ ideas about matter, the coherence of their emerging particle models, and how classroom science discourse influenced students’ learning. The study was conducted in two second grade classrooms in a rural Midwestern public school. We worked with the two teachers to help them design modeling activities for students to complement lessons from the Full Option Science System (FOSS™) science curriculum the teachers had previously used. Our data sources for student learning included individual interviews with students before and after they completed the set of Modeling in the Primary Grades (MPG) lessons, artifacts created by students during learning such as posters and science notebook entries, and videotapes of MPG lessons. Our findings suggest that second grade students who engaged in MPG model‐based inquiry lessons learned to use simple particle models to describe and explain a variety of material phenomena. For example, they could use particle models to account for differences in the appearance and behavior of solids, liquids, and gases and to explain what happens to matter during phase transitions. We also found variations in how MPG teachers structured classroom discourse, and our results suggest that such variations are associated with differences in the coherence of student models. © 2017 Wiley Periodicals, Inc. J Res Sci Teach 9999:988–1023, 2017